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Crystal structure of a lyase from alteromonas sp.

Analyse Crystal structure of a lyase from alteromonas sp. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6JQ9
Type: protein
Length: 965 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Short ulvan lyase
UniProt: A0A109PTH9
Ligands: CA, SO4
Pockets: 5 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Short ulvan lyase	protein	482	6% helix, 43% strand	A0A109PTH9
B	Short ulvan lyase	protein	483	6% helix, 44% strand	A0A109PTH9

Ligands and binding sites

CA · Calcium ion · metal · 4 copies · chains A, B
SO4 · Sulfate ion · ion · 3 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	994	0.76	0.79	79	empty
2	1077	0.75	0.78	85	empty
3	465	0.58	0.73	38	empty
4	94	0.36	0.75	21	SO4
5	55	0.31	0.76	10	empty

Interfaces

1 interface between chains.

A–B · 542 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

6JQ9 · Crystal structure of a lyase from Alteromonas sp. · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt A0A109PTH9
Elsewhere: RCSB PDB 6JQ9 · PDBe 6JQ9 · UniProt A0A109PTH9

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